Naruto: A Different Story
by DeathBloodBass
Summary: This story is set in a universe where Madara died in his final battle against Hashirama, but his loyal followers and ideals live on in hiding and gaining strength. Waiting for the day to make their appearance. Naruto's and Team Kakashi's storyline in this story is pretty much the same as the canon, thus this story will focus more on the supporting cast.


**NARUTO A DIFFERENT STORY  
** **Phantom Menance Arc Episode 1  
Return  
**

(This is basically AU. You are already aware that main story Madara survived his battle against Hashirama, but what if he was really killed and was not the only Uchiha who left Konoha. Such a small difference can change the storyline of the Main Story.)

* * *

 _Somewhere on the walls of Konoha..._

"So this is Konoha...", a cloaked man with a mask said.

"That's right, this is the first time you've ever come here.", a larger cloaked man said. "You're not having any second thoughts are you now?"

"No, but seeing the village that my ancestor created makes me feel nostalgic.", the masked man said when another cloaked figure appears before him. "Report."

"It's been confirmed. Kushina Uzumaki, the current Nine-Tails Jinchuuriki is pregnant and is due October 10th.", a female cloaked figure said.

"That'll be the time when the seal is the weakest.", the masked man said.

"So what to we do now? Our mission was to scout this village.", the large man said.

"We won't return yet.", the masked man said. "This is a perfect opportunity to test out the Leaf's fighting strength and see if all the peace made them weak."

* * *

 _Later on that very day..._

The figure cloaked figures along with two others stare at a cave guarded by ANBU Black Ops.

"Are you sure this is the place?", the female member asks. "I mean it could be a decoy."

"I'll check.", the young member said increasing his hearing abilities, but immediately falls done covering his ears after hearing.

"OH MY GOD IT HURTS, YA KNOOOOOWWWW!"

"Jeez, the woman have some strong lungs to scream like that."

"Alright then, I'm going in alone.", the masked man said standing up. "Prepare the next phase of the plan."

* * *

 _Inside the cave..._

"Alright! I know what you've been through but I need reseal the Nine-Tails." Minato said as Kushina nodded. He was preparing the hand signs till the two heard Biwako scream. "Biwako!" Minato yells as he look to see a masked man now holding Naruto who was still crying.

"You are the Fourth Hokage, Minato, if I recall. Step away from the Jinchuuriki or your son will die on the first minute he was born.", the masked man threatened with his hand over Naruto's head threatening to cast a jutsu on him. Minato stood still, knowing that the intruder isn't bluffing.

'How did he get past the guards and the barrier surrounding this place?', Minato thought starring at the man. "='I'm not seeing any kind to injury either. Who is he?'

"I won't ask again. Move! Or do you not value your son's life.", the masked man threaten once more with electricity surging from his hand. Minato then notice the fox trying to escape with the seal still incomplete. "Don't try anything."

"Wait, just stay calm." Minato said.

"Times up!", the masked man said as he throws Naruto up in the air and prepare of electrocute him.

"NARUTOOOOO!", Kushina yelled in her concern as Naruto cried but Minato caught him just in time.

"So the stories are true, but are you fast enough for this!", the masked man said setting off three Paper Bombs on Naruto's blanket. Minato grabs the blanket and disappear. "Now then..."

* * *

 _At the masked man's rendezous point..._

The masked man prepares to release the Nine-Tails.

"Are you able to control it? I mean you just got those eyes and haven't fully adjust to them.", the large man said.

"All the more reason to test them out and see how far I can go right now.", the masked man said activating his Sharingan. "It appears that it's your lucky day. I'm only able to control the beast at half strength. Still enough to destroy the village though. Come on out, Nine-Tails!"

Kushina screams as the Nine-Tails emerges from her, but the moment it came out the large man cuts the chakara line between the two leaving both with only half the power.

"Now then stall we.", the masked man said leaving with his group.

"Aren't you going to finish me off?", Kushina asks struggling to maintain conscious.

"Even I'm not heartless enough to kill an injured person. Even if that person is my enemy.", the masked man said. "Just be happy that you'll live. Can't leave a child growing without a mother."

* * *

 _Later..._

"Are you Madara Uchiha?", Minato asks the masked man.

"No, but the eye you see is indeed his.", the man answers. "I suppose you could way that I'm his successor, but if you want more information then you'll just have to beat it out of me, but be warned I defeated 1000 foes and not one of them managed to land a single injury on me."

'No doubt about it. He chakra is incredible, but not at the same level as Madara himself.', Minato thought. 'Not only that, but his four pals are no pushover either.'

* * *

" **Scorch Style: Blazing Sun**!", the female member said shooting large fireballs from the sleeves of her cloak, but Hiruzen easily deflects them with his staff.

'The fact that they're protecting the Nine-Tails from us confirms my suspicion that it's only having half it's original strength.', Hiruzen thought seeing the Leaf Ninjas having a better chance against the beast, but that doesn't mean they're out of the woods yet. 'Even so, it is still powerful and can still destroy the village, but right now I must focus on the foe in front of me. I don't know how, but she is able to use Ice, Wood, Scorch, Magnetic and Lava Style techniques. No one alive or dead is able to possess five Kekkei Genkai."

* * *

The other two members are fighting two of the Legendary Sannin, who were all called back to the village by the Third in case the Nine-Tails broke out.

"These guys are tougher than I thought.", Jiraiya said. "But from the looks of it they're also underestimating us at the same time."

"They probably think that the village gotten weak due to all the peace.", Tsunade said.

"Can't blame them for believing that.", Jiraiya chuckles. "It did happen to most place in the past, but the Hidden Leaf is not like them."

"Damn, I got careless and broke my arm!", one of the cloaked man said.

"Well what did you expect? The Sannin are Kage-Class Ninjas.", the other cloaked man said. "It's obvious that they would be tough."

* * *

"So you're Danzo.", the large cloaked man said staring at the old man.

"And you're one of the intruders who've released the Nine-Tails.", Danzo said. "I'm rather surprised that you know the time when the seal is at it's weakest and where the Jinchuuriki is. Tell me, what is your purpose here?"

"Originally just to scout the place, but our boss thought that we should test this village fighting capabilities as well."

"Is that so?", Danzo asks. "In that case, I better not disappoint him."

"You better not.", the large man said revealing six arms.

* * *

" **Rasengan**!", Minato yells as he hit the masked man's back with it and marked him with the Flying Raijin Seal. " **Flying Raijin Level 2**." Minato said as the masked man tried to get away but sees Minato in front of him and got stabbed with his kunai.

"Damn it! He must've marked me from where he struck me with his attack.', the man though before Minato placed another seal on him.

"You've earned my respect, Fourth Hokage.", the masked man said. "You're are first to have actually injured me. A feet which my last 1000 opponents have failed to do."

"Not only that, but I've also broke your connection to the fox.", Minato said.

"No matter. The purpose of this was to test the village's strength and I can see that if would be foolish to underestimate it."

"You've got that right."

"Because you've done something that even impressed me it's only fair you get something in return, since I have no intention of being captured.", the masked man said removing his mask and revealing his face. This shocks Minato greatly as it greatly resembles Madara in his youth.

"My name is Kaito Uchiha, the Second Coming of Madara Uchiha himself.", Kaito said. "On the day Madara died, you've all been deceived."

"I can only assume that Madara wan't the only Uchiha to leave the village.", Minato said.

"That is correct, since Madara was the biggest threat the rest who left with him were simply ignored."

"The fact that Madara attacked alone on the day he dies means that he made himself a martyr for those loyal to him."

"Yes, but I'm afraid that is all I can reveal now. You'll have to figure the rest out yourself.", Kaito said putting his mask on and toss a scroll to Minato. "This scroll contains a formula to seal Tailed-Beasts. I should know since I used it on the other Jinchuurikis when I was testing their capabilities."

"Hold on! Do you really think I'll just let you leave?!"

"You have no choice. With the Nine-Tails no longer under my control he's now just a wild beast."

'He's right, I have to time to waste.', Minato thought disappearing back to the village. Kaito shoots a flare signalling his teammates to retreat.

* * *

 _Leaf Village Border..._

Minato arrives in time to see the Nine-Tails preparing another Tail Beast Bomb. He prepares to summon Gamabunta till he heard.

" **Ninja Art! Bringing Down the House Jutsu!** " Gamahiro lands on top of the fox.

"Sensei!", Minato called out in joy to see his master, Jiraiya arrive when he did.

"Sorry, I'm late but that weird cloak guy and his pals ran off after seeing the flare.", Jiraiya said.

'That means that he's done here for now, but I have no doubt that he'll return.', Minato thought. 'But right now I have bigger things to worry about. I just hope this formula he gave me is legit.'

"Minato!", Minato and Jiraiya turn to see the Hiruzen calling him. "How did this happen?"

"I'll explain later.", Minato said as Sarutobi grabs on to him and used Flying Raijin to transport themselves away from the village. Minato pulls Kushina and Naruto out in time as the Nine-Tails fall down. "Damn my chakra is running low. I used too much in my fight with that man."

"Minato we need to seal the fox again.", Kushina said forming a barrier with her chakra chains.

"Kushina, are you alright?", Minato asks in worry.

"Don't worry. That man was only able to control the Nine-Tails at half-power, thus was forced to leave the remaining half inside me. Because it wasn't fully extracted I was able to survive.", Kushina said.

"Alright, originally I plan to use that jutsu to seal the fox, but first I'll give this jutsu he gave me a try.", Minato said opening the scroll, reads it quickly, stares at it with amazement. "Incredible. This jutsu is absolute genius. I'm sorry Kushina, but I'm going to need Naruto for this."

"I understand.", Kushina said handing Naruto to Minato.

"Naruto, I apologize for the burden I'm going to give you, but one day you'll become a ninja capable of great things.", Minato said placing Naruto onto the pedestal. He then performs the hand signs written from the scroll and cast the jutsu.

"No! No! Not this again!", The Nine-Tails roar as he struggle to break free of his chains, but to no avail due to only being at half strength. The Nine-Tails was then sealed into Naruto. "NOOOOOO!"

Naruto felt the sudden surge of power along with that sudden yell and start crying again. Kushina regains her composure and grab Naruto comforting him, while the others sigh in relief.

"It's finally over.", Minato said.

"You think this is over!", the Nine-Tails voice calls out in rage shocking the group.

Minato and the others could look in fear, but that fear turns to surprise after seeing the Nine-Tails the size of a puppy.

"What the hell happened to me?!", the Nine-Tails cries upon finding himself chibi before Jiraiya picks him up by the neck.

"It appears that the Nine-Tails is able to make a physical form even though he is in a host body, but he appears to be helpless.", Jiraiya said.

"I'll show you helpless!", the Nine-Tails said biting Jiraiya's finger.

"YEOW!"

* * *

Minato called a meeting with the Village Council with Hiruzen, Jiraiya and Tsunade participating as well.

"So the attacker was indeed an Uchiha?", Hiruzen asks.

"Yes and not only that, but he also possess Madara's Sharingan eyes.", Minato said. "This further proves that he is the spiritual successor of Madara himself."

"That fact that he is only able to control the Nine-Tails at full strength can only mean that he hasn't fully adjusted to the power of the eyes.", Danzo said. "But what concerns me the most is that there are Uchihas still loyal to Madara's cause."

"It's not surprising. Madara was the biggest threat at that time, so it was easy for his followers to slip out and go into hiding.", Minato said.

"If that's the case, then what worries me the most is what they have been doing between then and now.", Jiraiya said. "With such a time gap even a small group will grow in numbers and strength, and form a powerful organization."

"But why go as far as make someone a new Madara Uchiha?", Koharu asks.

"Madara Uchiha was symbol of the Uchiha Clan and a name that strikes fear to the heart of the enemy.", Tsunade said. "It's common for those to take a famous shinobi's name for themselves, but I fear that this time Kaito is the closest of being a true copy Madara."

"Are the Uchiha planning to continue Madara's goal?", Koharu asks.

"The real question is when will it happen?", Minato said gravely.


End file.
